Mercurial > repos > richard-burhans > segalign
diff segalign.xml @ 14:f9e91add973c draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit eb6ee047d39760f2596b6e343e2dc3898fafc5cd
| author | richard-burhans |
|---|---|
| date | Mon, 29 Jul 2024 20:53:43 +0000 |
| parents | e6fde4082c76 |
| children | 99ee8d6f6815 |
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--- a/segalign.xml Sat Jul 13 16:51:52 2024 +0000 +++ b/segalign.xml Mon Jul 29 20:53:43 2024 +0000 @@ -8,7 +8,6 @@ <import>ungapped_extension_options.xml</import> <import>gapped_extension_options.xml</import> <import>output_options.xml</import> - <import>segalign_output_options.xml</import> <import>system_options.xml</import> </macros> <expand macro="edam_ontology"/> @@ -20,235 +19,135 @@ <include path="runner.py"/> </required_files> <command detect_errors="exit_code"><![CDATA[ -## -## https://www.gnu.org/software/coreutils/manual/html_node/nproc-invocation.html -## -## If the OMP_NUM_THREADS or OMP_THREAD_LIMIT environment variables -## are set, then they will determine the minimum and maximum returned -## value respectively. -## -## This is how you tame nproc(1) -## -OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2} +## Convert input to 2bit for lastz ------------------------------------- -## Mode ---------------------------------------------------------------- +mkdir -p "\$(pwd)/work" && +faToTwoBit <(gzip -cdfq '$target') "\$(pwd)/work/ref.2bit" && +faToTwoBit <(gzip -cdfq '$query') "\$(pwd)/work/query.2bit" && -#if str($mode.mode_selector) == "segalign" - #if str($mode.gapped_extension_options.nogapped) == "false" - mkdir -p "\$(pwd)/work" && - faToTwoBit <(gzip -cdfq '$mode.target') "\$(pwd)/work/ref.2bit" && - faToTwoBit <(gzip -cdfq '$mode.query') "\$(pwd)/work/query.2bit" && - #end if - #if str($mode.diagonal_partition_options.diagonal_partition) == "true" - #set $segalign_mode = "segalign_diagonal_partition" - ## explicitly calling python to bypass a pulsar bug - ## https://github.com/galaxyproject/pulsar/issues/341 - python '$__tool_directory__/runner.py' - --output-type tarball - --output-file '$segalign_diagonal_partition_output' - --diagonal-partition - --num-cpu \${GALAXY_SLOTS:-2} - --tool_directory '$__tool_directory__' - #else - #set $segalign_mode = "segalign" - python '$__tool_directory__/runner.py' - --output-type output - --output-file '$segalign_output' - --num-cpu \${GALAXY_SLOTS:-2} - --tool_directory '$__tool_directory__' - #end if - '$mode.target' - '$mode.query' -#else if str($mode.mode_selector) == "segalign_repeat_masker" - #set $segalign_mode = "segalign_repeat_masker" - run_segalign_repeat_masker - '$mode.seq_file' - --num_cpu \${GALAXY_SLOTS:-2} -#end if +## explicitly calling python to bypass a pulsar bug +## https://github.com/galaxyproject/pulsar/issues/341 +python '$__tool_directory__/runner.py' + --output-type tarball + --output-file '$segalign_output' + --diagonal-partition + --num-cpu \${GALAXY_SLOTS:-2} + --tool_directory '$__tool_directory__' + '$target' + '$query' ## Sequence Options ---------------------------------------------------- - --strand '$mode.sequence_options.strand_selector' -#if $segalign_mode == "segalign_repeat_masker" - --neighbor_proportion '$mode.sequence_options.neighbor_proportion' -#end if + --strand '$sequence_options.strand_selector' ## Scoring Options ----------------------------------------------------- -#set $scoring_pathname = str($mode.scoring_options.scoring) +#set $scoring_pathname = str($scoring_options.scoring) #if $scoring_pathname != "None": - --scoring '$scoring_pathname' + --scoring '$scoring_pathname' #end if -#if str($mode.scoring_options.ambiguous_selector) != "x" - #if str($mode.scoring_options.set_ambiguous_params_selector) == "true" - #set $argument_value = ','.join($mode.scoring_options.ambiguous_selector, $mode.scoring_options.ambiguous_reward, $mode.scoring_options.ambiguous_penalty) - --ambiguous '$argument_value' +#if str($scoring_options.ambiguous_selector) != "x" + #if str($scoring_options.set_ambiguous_params_selector) == "true" + #set $argument_value = ','.join($scoring_options.ambiguous_selector, $scoring_options.ambiguous_reward, $scoring_options.ambiguous_penalty) + --ambiguous '$argument_value' #else - --ambiguous '$ambiguous_selector' + --ambiguous '$ambiguous_selector' #end if #end if ## Seeding Options ----------------------------------------------------- -#if str($mode.seeding_options.seed.seed_selector) == "custom" - --seed '$mode.seeding_options.seed.custom_seed' +#if str($seeding_options.seed.seed_selector) == "custom" + --seed '$seeding_options.seed.custom_seed' #else - --seed '$mode.seeding_options.seed.seed_selector' + --seed '$seeding_options.seed.seed_selector' #end if - --step '$mode.seeding_options.step' -#if str($mode.seeding_options.notransition) == "true" - --notransition + --step '$seeding_options.step' +#if str($seeding_options.notransition) == "true" + --notransition #end if ## Ungapped Extension Options ------------------------------------------ - --xdrop '$mode.ungapped_extension_options.xdrop' - --hspthresh '$mode.ungapped_extension_options.hspthresh' -#if str($mode.ungapped_extension_options.noentropy) == "true" - --noentropy + --xdrop '$ungapped_extension_options.xdrop' + --hspthresh '$ungapped_extension_options.hspthresh' +#if str($ungapped_extension_options.noentropy) == "true" + --noentropy #end if ## Gapped Extension Options -------------------------------------------- -#if $segalign_mode != "segalign_repeat_masker" - #if str($mode.gapped_extension_options.nogapped) == "true" - --nogapped - #end if - --ydrop '$mode.gapped_extension_options.ydrop' - #if str($mode.gapped_extension_options.gappedthresh) != "" - --gappedthresh '$mode.gapped_extension_options.gappedthresh' - #end if - #if str($mode.gapped_extension_options.notrivial) == "true" - --notrivial - #end if + --nogapped + --ydrop '$gapped_extension_options.ydrop' +#if str($gapped_extension_options.gappedthresh) != "" + --gappedthresh '$gapped_extension_options.gappedthresh' +#end if +#if str($gapped_extension_options.notrivial) == "true" + --notrivial #end if ## Output Options ----------------------------------------------------- -#if $segalign_mode != "segalign_repeat_masker" - #if str($mode.output_options.format.format_selector) == "bam" - --format '$mode.output_options.format.bam_options' - #else if str($mode.output_options.format.format_selector) == "general_def" - --format general- - #else if str($mode.output_options.format.format_selector) == "general_full" - --format 'general-:${mode.output_options.format.fields}' - #else if str($mode.output_options.format.format_selector) == "maf" - --format '$mode.output_options.format.maf_type' - #else if str($mode.output_options.format.format_selector) == "blastn" - --format=BLASTN- - #else if str($mode.output_options.format.format_selector) == "differences" - --format=differences - #end if +#if str($output_options.format.format_selector) == "bam" + --format '$output_options.format.bam_options' +#else if str($output_options.format.format_selector) == "general_def" + --format general- +#else if str($output_options.format.format_selector) == "maf" + --format '$output_options.format.maf_type' +#else if str($output_options.format.format_selector) == "blastn" + --format=BLASTN- +#else if str($output_options.format.format_selector) == "general_full" + --format 'general-:${output_options.format.fields}' +#else if str($output_options.format.format_selector) == "differences" + --format=differences +#end if ## todo :: rplot, bam ## --action:target=multiple ## $output_format.rplot - ## .if str( $output_format.out.format ) == "bam": + ## #if str( $output_format.out.format ) == "bam": ## | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}' - ## .else: + ## #else: ## > '${output}' - ## .end if - ## .if $output_format.rplot: + ## #end if + ## #if $output_format.rplot: ## && ## Rscript $r_plot > /dev/null 2>&1 - ## .end if -#else if $segalign_mode == "segalign_repeat_masker" - --M '$mode.output_options.M' - --output '$segalign_repeat_masker_output' -#end if -#if str($mode.output_options.markend) == "true" - --markend -#end if + ## #end if ## System Options ----------------------------------------------------- - --wga_chunk_size '$mode.system_options.wga_chunk_size' - --lastz_interval_size '$mode.system_options.lastz_interval_size' - --seq_block_size '$mode.system_options.seq_block_size' - --num_gpu '$mode.system_options.num_gpu' -#if str($mode.system_options.debug) == "true" - --debug + --wga_chunk_size '$system_options.wga_chunk_size' + --lastz_interval_size '$system_options.lastz_interval_size' + --seq_block_size '$system_options.seq_block_size' + --num_gpu '$system_options.num_gpu' +#if str($system_options.debug) == "true" + --debug #end if -## ------------------------------------------------------------------- +## Package Output ---------------------------------------------------- -#if $segalign_mode == "segalign_diagonal_partition" - && - python '$__tool_directory__/package_output.py' - --tool_directory '$__tool_directory__' -#end if + && python '$__tool_directory__/package_output.py' ]]></command> <inputs> - <conditional name="mode"> - <param name="mode_selector" type="select" label="Choose the mode"> - <option value="segalign" selected="true">SegAlign</option> - <option value="segalign_repeat_masker">SegAlign repeat masker</option> - </param> - <when value="segalign"> - <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/> - <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/> - <expand macro="sequence_options"/> - <expand macro="scoring_options"/> - <expand macro="seeding_options"/> - <expand macro="ungapped_extension_options"/> - <expand macro="gapped_extension_options"/> - <expand macro="output_options"> - <expand macro="segalign_output_options"/> - </expand> - <expand macro="system_options"/> - <section name="diagonal_partition_options" expanded="false" title="Diagonal Partition Options"> - <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/> - </section> - </when> - <when value="segalign_repeat_masker"> - <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/> - <expand macro="sequence_options"> - <param argument="--neighbor_proportion" type="float" value="0.2" label="Proportion of neighbouring intervals to align the query interval to"/> - </expand> - <expand macro="scoring_options"/> - <expand macro="seeding_options"/> - <expand macro="ungapped_extension_options"/> - <expand macro="output_options"> - <param argument="--M" type="integer" value="1" max="255" label="report any position that is covered by at least this many alignments; the maximum allowed depth is 255"/> - </expand> - <expand macro="system_options"/> - </when> - </conditional> + <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/> + <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/> + <expand macro="sequence_options"/> + <expand macro="scoring_options"/> + <expand macro="seeding_options"/> + <expand macro="ungapped_extension_options"/> + <expand macro="gapped_extension_options"/> + <expand macro="output_options"/> + <expand macro="system_options"/> </inputs> <outputs> - <data name="segalign_output" format="tabular" label="SegAlign on ${on_string}"> - <change_format> - <when input="mode.output_options.format.format_selector" value="bam" format="bam"/> - <when input="mode.output_options.format.format_selector" value="maf" format="maf"/> - <when input="mode.output_options.format.format_selector" value="differences" format="interval"/> - </change_format> - <filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is False</filter> - </data> - <data name="segalign_diagonal_partition_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign Diagonal Partition on ${on_string}"> - <filter>mode['mode_selector'] == 'segalign' and mode['diagonal_partition_options']['diagonal_partition'] is True</filter> - </data> - <data name="segalign_repeat_masker_output" format="tabular" label="SegAlign Repeat Masker on ${on_string}"> - <filter>mode['mode_selector'] == 'segalign_repeat_masker'</filter> - </data> + <data name="segalign_output" format="tgz" from_work_dir="data_package.tgz" label="SegAlign on ${on_string}"/> </outputs> <tests> <test expect_num_outputs="1" expect_test_failure="true"> - <param name="mode_selector" value="segalign"/> <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> - <output name="segalign_output" decompress="true" file="segalign-output.maf.gz" ftype="maf"/> - </test> - <test expect_num_outputs="1" expect_test_failure="true"> - <param name="mode_selector" value="segalign_repeat_masker"/> - <param name="seq_file" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> - <output name="segalign_repeat_masker_output" decompress="true" file="segalign-repeat-masker-output.tab.gz" ftype="tabular"/> - </test> - <test expect_num_outputs="1" expect_test_failure="true"> - <param name="mode_selector" value="segalign"/> - <param name="target" value="hg38.chr20.chunk.fa.gz" ftype="fasta.gz"/> - <param name="query" value="mm39.chr2.chunk.fa.gz" ftype="fasta.gz"/> - <param name="diagonal_partition" value="true"/> - <output name="segalign_diagonal_partition_output" ftype="tgz"> + <output name="segalign_output" ftype="tgz"> <assert_contents> <has_archive_member path="galaxy/commands.json"/> </assert_contents>